This file provides an overview of the types of figures that one can potentially generate from each feature category to gain insight into the features associating with disease conditions (Section 1).
Section 2 then runs an association study using the given features and sample conditions and plots the key features from each feature category using a representative figure.

The purpose is not to provide a comprehensive analysis in a single HTML but to help point directions for future investigation.

1 Overview of the association study result

Here we provide a brief overview of the association study result, including the number of features in each feature type, and the number of features that are significantly associated ( P-value < 0.1) with the conditions of the interest.

2 Cell type proportions

knitr::include_graphics( system.file("extdata/figure", "celltypeproportion_example_figures.png",   package = "scFeatures")  )

  1. Barplot shows the composition of cells types
  2. Boxplot shows the top cell types that differs between conditions
  3. PCA plot shows the separation of conditions based on the cell type proportion features

2.1 Composition barplot

2.2 Boxplot of top features

## [1] "up regulated in Responder"

2.3 PCA plot

3 Cell type specific gene expressions

knitr::include_graphics( system.file("extdata/figure",  "celltypegene_example_figures.png" ,   package = "scFeatures")  )

  1. Heatmaps shows the top cell type specific gene expression features that differs between conditions
  2. MA plot shows the expression and log2 fold change of the cell type specific gene expression features
  3. Volcano plot shows the log2 fold change and P-values of the cell type specific gene expression features
  4. PCA plot shows the separation of conditions based on the cell type specific gene expression features
  5. Dot plot shows the pathway enrichment of the top cell type specific gene expression features that differs between conditions
  6. Enrichment map of the top cell type specific gene expression features that differs between conditions
  7. Functional grouping of the top cell type specific gene expression features that differs between conditions

3.1 Heatmap

## [1] "up regulated in Responder"

3.2 MA plot

3.3 Volcano plot

3.4 PCA plot

3.5 Dot plot

## [1] "up regulated"

3.6 Enrichment map

3.7 Functional grouping

4 Cell type specific pathway expressions

knitr::include_graphics(  system.file("extdata/figure",  "pathway_example_figures.png" ,   package = "scFeatures")    )

1. Heatmaps shows the top cell type specific pathway expression features that differs between conditions
2. Boxplot shows the top cell type specific pathway expression features that differs between conditions
3. PCA plot shows the separation of conditions based on the cell type specific pathway expression features

4.1 Heatmap

## [1] "up regulated in Responder"

4.2 Boxplot

## [1] "up regulated in Responder"

4.3 PCA plot

5 Cell type specific cell-cell communications

knitr::include_graphics(  system.file("extdata/figure",  
                   "CCI_example_figures.png"  ,   package = "scFeatures")    )

1. Heatmap shows the top cell cell interactions features that differs between conditions
2. Heatmap shows the difference in the number of interactions between conditions
3. PCA plot shows the separation of conditions based on the cell type specific pathway expression features
4. Network plot shows the difference in the number of interactions between conditions 5. Boxplot shows the top cell cell interaction features that differs between conditions

5.1 Heatmap of top cell cell interactions

## [1] "up regulated in Responder"

5.2 Heatmap of difference in number of interactions

5.3 PCA plot

5.4 Network plot

5.5 Boxplot

## [1] "up regulated in Responder"

6 Overall aggregated gene expressions

knitr::include_graphics(  system.file("extdata/figure",  
         "aggregatedgene_example_figures.png" ,   package = "scFeatures")    )

  1. Heatmaps shows the top aggregated gene expression features that differs between conditions
  2. MA plot shows the expression and log2 fold change of the aggregated gene expression features
  3. Volcano plot shows the log2 fold change and P-values of the aggregated gene expression features
  4. PCA plot shows the separation of conditions based on the aggregated gene expression features
  5. Dot plot shows the pathway enrichment of the top aggregated gene expression features that differs between conditions
  6. Enrichment map of the top aggregatedgene expression features that differs between conditions
  7. Functional grouping of the top aggregated gene expression features that differs between conditions

6.1 Heatmap

## [1] "up regulated in Responder"

6.2 MA plot

6.3 Volcano plot

6.4 PCA plot

6.5 Dot plot

## [1] "up regulated"

6.6 Enrichment map

6.7 Functional grouping

7 Spatial metrics

knitr::include_graphics(  system.file("extdata/figure",  
       "spatial_example_figures.png",   package = "scFeatures")    )

  1. Heatmaps shows the top spatial features that differs between conditions
  2. Boxplot shows the top spatial features that differs between conditions
  3. PCA plot shows the separation of conditions based on the spatial features

7.1 Heatmap

## [1] "up regulated in WT"

7.2 Boxplot

## [1] "up regulated in WT"

7.3 PCA plot